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Yorodumi- PDB-4rwa: Synchrotron structure of the human delta opioid receptor in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rwa | ||||||
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Title | Synchrotron structure of the human delta opioid receptor in complex with a bifunctional peptide (PSI community target) | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Human opioid receptor / bifunctional peptide / GPCR signaling / GPCR network / PSI-Biology / Structural Genomics / GPCR / membrane / Lipidic cubic phase / BRIL | ||||||
Function / homology | Function and homology information electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å | ||||||
Authors | Fenalti, G. / Zatsepin, N.A. / Betti, C. / Giguere, P. / Han, G.W. / Ishchenko, A. / Liu, W. / Guillemyn, K. / Zhang, H. / James, D. ...Fenalti, G. / Zatsepin, N.A. / Betti, C. / Giguere, P. / Han, G.W. / Ishchenko, A. / Liu, W. / Guillemyn, K. / Zhang, H. / James, D. / Wang, D. / Weierstall, U. / Spence, J.C.H. / Boutet, S. / Messerschmidt, M. / Williams, G.J. / Gati, C. / Yefanov, O.M. / White, T.A. / Oberthuer, D. / Metz, M. / Yoon, C.H. / Barty, A. / Chapman, H.N. / Basu, S. / Coe, J. / Conrad, C.E. / Fromme, R. / Fromme, P. / Tourwe, D. / Schiller, P.W. / Roth, B.L. / Ballet, S. / Katritch, V. / Stevens, R.C. / Cherezov, V. / GPCR Network (GPCR) | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2015 Title: Structural basis for bifunctional peptide recognition at human delta-opioid receptor. Authors: Fenalti, G. / Zatsepin, N.A. / Betti, C. / Giguere, P. / Han, G.W. / Ishchenko, A. / Liu, W. / Guillemyn, K. / Zhang, H. / James, D. / Wang, D. / Weierstall, U. / Spence, J.C. / Boutet, S. / ...Authors: Fenalti, G. / Zatsepin, N.A. / Betti, C. / Giguere, P. / Han, G.W. / Ishchenko, A. / Liu, W. / Guillemyn, K. / Zhang, H. / James, D. / Wang, D. / Weierstall, U. / Spence, J.C. / Boutet, S. / Messerschmidt, M. / Williams, G.J. / Gati, C. / Yefanov, O.M. / White, T.A. / Oberthuer, D. / Metz, M. / Yoon, C.H. / Barty, A. / Chapman, H.N. / Basu, S. / Coe, J. / Conrad, C.E. / Fromme, R. / Fromme, P. / Tourwe, D. / Schiller, P.W. / Roth, B.L. / Ballet, S. / Katritch, V. / Stevens, R.C. / Cherezov, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rwa.cif.gz | 307.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rwa.ent.gz | 250.1 KB | Display | PDB format |
PDBx/mmJSON format | 4rwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rwa_validation.pdf.gz | 641.8 KB | Display | wwPDB validaton report |
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Full document | 4rwa_full_validation.pdf.gz | 647 KB | Display | |
Data in XML | 4rwa_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 4rwa_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/4rwa ftp://data.pdbj.org/pub/pdb/validation_reports/rw/4rwa | HTTPS FTP |
-Related structure data
Related structure data | 4rwdC 4n6hS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN |
-Components
#1: Protein | Mass: 45636.812 Da / Num. of mol.: 2 / Mutation: M29W, H124I, R138L,M29W, H124I, R138L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human) Gene: cybC, OPRD, OPRD1, cybC / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P0ABE7 #2: Protein/peptide | #3: Chemical | ChemComp-OLC / ( | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 21 |
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-Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.18 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6 Details: 25-28% (v/v) PEG 400, 0.12 to 0.2 M NaCl, 100 mM MES buffer at pH 6.0, 1 mM DIPP-NH2 and 5% (v/v) of either one of the following additives: 30% glycerol, 1.0 M glycine or 0.01M L-glutathione ...Details: 25-28% (v/v) PEG 400, 0.12 to 0.2 M NaCl, 100 mM MES buffer at pH 6.0, 1 mM DIPP-NH2 and 5% (v/v) of either one of the following additives: 30% glycerol, 1.0 M glycine or 0.01M L-glutathione reduced/0.01M L-glutathione oxidized, Lipidic cubic phase, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 8, 2013 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.28→94.61 Å / Num. obs: 18862 / % possible obs: 96.3 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.173 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 3.3→3.51 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.875 / Mean I/σ(I) obs: 1.9 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4N6H Resolution: 3.28→94.61 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.899 / SU B: 58.708 / SU ML: 0.445 / Cross valid method: THROUGHOUT / ESU R Free: 0.534 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90.825 Å2
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Refinement step | Cycle: LAST / Resolution: 3.28→94.61 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 3.282→3.367 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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